Chryseomicrobium excrementi (KCTC 33943, LMG 30119, JCM 32415)

Name: Chryseomicrobium excrementi (KCTC 33943, LMG 30119, JCM 32415)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159857

Type strain

Strain Designation ET03

Culture col. no. KCTC 33943 LMG 30119 JCM 32415 ET03 MCC 3378

NCBI tax ID(s) 2041346

Special Collections JCM KCTC Literature strains

Links

Chryseomicrobium excrementi ET03 is an aerobe, spore-forming, Gram-positive prokaryote that forms circular colonies and was isolated from cast of an earthworm .

spore-forming Gram-positive rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 283932

LMG 30119,KCTC 33943,JCM 32415

@ref 20215

Last LPSN update 2025-12-16 10:08:21

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Caryophanaceae

Genus Chryseomicrobium

Species Chryseomicrobium excrementi

Full scientific name Chryseomicrobium excrementi Saha et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
66561	positive	1.0-2.0 µm	0.5 µm	rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
66561	golden yellow	circular	<1 day	LB agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
66561	LB (Luria-Bertani) agar

Culture temp

@ref	Growth	Type	Temperature (°C)
66561	positive	growth	20-40
66561	positive	optimum	35-37
67770	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH
66561	positive	optimum	7
66561	positive	growth	6-9

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
66561	aerobe
67771	aerobe
125439	obligate aerobe

Spore formation

66561

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66561	NaCl	positive	growth	0-8 %
66561	NaCl	positive	optimum	2 %

Observation

67770

Observationquinones: MK-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66561	30796 ChEBI	(R)-malic acid	-	assimilation
66561	16651 ChEBI	(S)-lactate	-	assimilation
66561	16810 ChEBI	2-oxoglutarate	-	assimilation
66561	73918 ChEBI	3-O-methyl-D-glucose	+	assimilation
66561	30566 ChEBI	4-aminobutyrate	-	assimilation
66561	16411 ChEBI	acetic acid	+	assimilation
66561	13705 ChEBI	acetoacetate	+	assimilation
66561	73706 ChEBI	bromosuccinate	-	assimilation
66561	17057 ChEBI	cellobiose	-	assimilation
66561	17057 ChEBI	cellobiose	-	builds acid from
66561	53258 ChEBI	citric acid	-	assimilation
66561	18333 ChEBI	D-arabitol	+	assimilation
66561	29990 ChEBI	D-aspartate	-	assimilation
66561	15824 ChEBI	D-fructose	+	assimilation
66561	78697 ChEBI	D-fructose 6-phosphate	-	assimilation
66561	28847 ChEBI	D-fucose	-	assimilation
66561	12936 ChEBI	D-galactose	-	assimilation
66561	18024 ChEBI	D-galacturonic acid	-	assimilation
66561	30612 ChEBI	D-glucarate	-	assimilation
66561	8391 ChEBI	D-gluconate	+	assimilation
66561	14314 ChEBI	D-glucose 6-phosphate	+	assimilation
66561	15748 ChEBI	D-glucuronate	-	assimilation
66561	16899 ChEBI	D-mannitol	-	assimilation
66561	16024 ChEBI	D-mannose	-	assimilation
66561	16523 ChEBI	D-serine	-	assimilation
66561	17924 ChEBI	D-sorbitol	-	assimilation
66561	15740 ChEBI	formate	-	assimilation
66561	28757 ChEBI	fructose	+	builds acid from
66561	16537 ChEBI	galactarate	-	assimilation
66561	5291 ChEBI	gelatin	-	assimilation
66561	5291 ChEBI	gelatin	+	hydrolysis
66561	28066 ChEBI	gentiobiose	-	assimilation
66561	17234 ChEBI	glucose	+	builds acid from
66561	32323 ChEBI	glucuronamide	-	assimilation
66561	17754 ChEBI	glycerol	-	assimilation
66561	70744 ChEBI	glycine-proline	-	assimilation
66561	17596 ChEBI	inosine	-	assimilation
66561	15443 ChEBI	inulin	-	builds acid from
66561	16977 ChEBI	L-alanine	-	assimilation
66561	29991 ChEBI	L-aspartate	+	assimilation
66561	18287 ChEBI	L-fucose	-	assimilation
66561	29985 ChEBI	L-glutamate	+	assimilation
66561	15971 ChEBI	L-histidine	-	assimilation
66561	15589 ChEBI	L-malate	+	assimilation
66561	18183 ChEBI	L-pyroglutamic acid	+	assimilation
66561	62345 ChEBI	L-rhamnose	+	assimilation
66561	17115 ChEBI	L-serine	-	assimilation
66561	17716 ChEBI	lactose	-	assimilation
66561	17306 ChEBI	maltose	+	builds acid from
66561	37684 ChEBI	mannose	-	builds acid from
66561	28053 ChEBI	melibiose	-	assimilation
66561	28053 ChEBI	melibiose	-	builds acid from
66561	74611 ChEBI	methyl (R)-lactate	-	assimilation
66561	37657 ChEBI	methyl D-glucoside	-	assimilation
66561	51850 ChEBI	methyl pyruvate	-	assimilation
66561	17268 ChEBI	myo-inositol	+	assimilation
66561	28800 ChEBI	N-acetylgalactosamine	-	assimilation
66561	59640 ChEBI	N-acetylglucosamine	-	assimilation
66561	35418 ChEBI	n-acetylneuraminate	-	assimilation
66561	17632 ChEBI	nitrate	+	reduction
66561	17309 ChEBI	pectin	-	assimilation
66561	17272 ChEBI	propionate	-	assimilation
66561	26490 ChEBI	quinate	+	assimilation
66561	16634 ChEBI	raffinose	-	assimilation
66561	17814 ChEBI	salicin	+	assimilation
66561	17814 ChEBI	salicin	+	builds acid from
66561	17164 ChEBI	stachyose	-	assimilation
66561	28017 ChEBI	starch	-	hydrolysis
66561	17992 ChEBI	sucrose	-	assimilation
66561	17992 ChEBI	sucrose	-	builds acid from
66561	27082 ChEBI	trehalose	-	assimilation
66561	27082 ChEBI	trehalose	-	builds acid from
66561	32528 ChEBI	turanose	-	assimilation
66561	53423 ChEBI	tween 40	-	assimilation

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is resistant
66561	1 % sodium lactate
66561	aztreonam
66561	D-serine
66561	fusidate
66561	guanidinium chloride
66561	lincomycin
66561	lithium chloride
66561	minocycline
66561	nalidixic acid
66561	niaproof
66561	potassium tellurite
66561	sodium butyrate
66561	tetrazolium blue
66561	troleandomycin
66561	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66561	15688 ChEBI	acetoin

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
66561	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
66561	catalase	-	1.11.1.6
66561	cytochrome oxidase	-	1.9.3.1
66561	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

@ref

66561

Fatty acid	Percentage
C15:0 iso	45
C16:1 w7c OH	13
C16:0 iso	11.8
C14:0 iso	6.2
C15:0 anteiso	3.4
C17:0 iso	2.2
C16:0	1.8
C17:0 anteiso	1.6
C16:1 w11c	1.2
C17:1 iso / C17:1 anteiso	0.9
C16:1 w7c / C16:1 w6c	0.6
C14:0	0.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration
66561	cast of an earthworm (Eisenia fetida)	Centre of Floriculture and Agribusiness Management of University of North Bengal at Siliguri, West Bengal	India	IND	Asia	26.7072	88.3558 26.7072/88.3558	LB agar	over night
67770	Cast of an earthworm (Eisenia fetida) reared at the Centre of Floriculture and Agribusiness Management of University of North Bengal at Siliguri	West Bengal	India	IND	Asia
67771	From freshly liberated cast of Eisenia fetida, Campus area of University of North Bengal	Siliguri, West Bengal	India	IND	Asia

Taxonmaps

69479

Global distribution of 16S sequence KU230523 (>99% sequence identity) for Planococcaceae from Microbeatlas

Aquatic Samples	124
Soil Samples	56
Animal Samples	360
Plant Samples	6
Total Samples	546

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM279830v1 assembly for Chryseomicrobium excrementi ET03	scaffold	GCA_002798305	2041346.3	2882380101	2041346	73.1

Genome browser: GCA_002798305

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66561	Chryseomicrobium excrementi 16S ribosomal RNA gene, partial sequence	KU230523.2	1517		2041346
67770	Chryseomicrobium excrementi 16S ribosomal RNA gene, partial sequence	KU230523	1517		2041346

GC content

@ref	GC-content (mol%)	Method
66561	42.90	genome sequence analysis
67770	42.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chryseomicrobium excrementi ET03
NCBI: GCA_002798305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	66.40	no
125439	motility	BacteriaNetⓘ	no	57.10	no
125439	gram_stain	BacteriaNetⓘ	variable	69.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chryseomicrobium sp. ET03
PATRIC: 2041346.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	76.86	yes
125438	anaerobic	anaerobicⓘ	no	97.21	yes
125438	spore-forming	spore-formingⓘ	yes	56.62	no
125438	aerobic	aerobicⓘ	yes	82.95	yes
125438	thermophilic	thermophileⓘ	no	93.58	yes
125438	flagellated	motile2+ⓘ	yes	53.07	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chryseomicrobium excrementi sp. nov., a Gram-stain-positive rod-shaped bacterium isolated from an earthworm (Eisenia fetida) cast.	Saha T, Chakraborty B, Das S, Thakur N, Chakraborty R	Int J Syst Evol Microbiol	10.1099/ijsem.0.002791	2018

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#66561	Tilak Saha, Biswanath Chakraborty, Sayak Das, Nagendra Thakur and Ranadhir Chakraborty: Chryseomicrobium excrementi sp. nov., a Gram-stain-positive rod-shaped bacterium isolated from an earthworm (Eisenia fetida) cast. IJSEM 68: 2165 - 2171 2018 ( DOI 10.1099/ijsem.0.002791 , PubMed 29749923 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Chryseomicrobium excrementi (KCTC 33943, LMG 30119, JCM 32415)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile?

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002798305

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

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Fatty acid profile